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- PDB-8v6t: Crystal structure of EcThsB2 -

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Basic information

Entry
Database: PDB / ID: 8v6t
TitleCrystal structure of EcThsB2
ComponentsMolecular chaperone Tir
KeywordsIMMUNE SYSTEM / Antiphage immunity / nucleotide signalling
Function / homologyThoeris protein ThsB, TIR-like domain / Thoeris protein ThsB, TIR-like domain / BROMIDE ION / Molecular chaperone Tir
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.98 Å
AuthorsShi, Y. / Masic, V. / Mosaiab, T. / Goulart, C.C. / Hartley-Tassell, L. / Sorbello, M. / Vasquez, E. / Mishra, B.P. / Holt, S. / Gu, W. ...Shi, Y. / Masic, V. / Mosaiab, T. / Goulart, C.C. / Hartley-Tassell, L. / Sorbello, M. / Vasquez, E. / Mishra, B.P. / Holt, S. / Gu, W. / Kobe, B. / Ve, T.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)FT200100572 Australia
CitationJournal: Sci Adv / Year: 2024
Title: Structural characterization of macro domain-containing Thoeris antiphage defense systems.
Authors: Shi, Y. / Masic, V. / Mosaiab, T. / Rajaratman, P. / Hartley-Tassell, L. / Sorbello, M. / Goulart, C.C. / Vasquez, E. / Mishra, B.P. / Holt, S. / Gu, W. / Kobe, B. / Ve, T.
History
DepositionDec 2, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Molecular chaperone Tir
B: Molecular chaperone Tir
C: Molecular chaperone Tir
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,75310
Polymers59,1943
Non-polymers5597
Water4,432246
1
A: Molecular chaperone Tir
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9714
Polymers19,7311
Non-polymers2403
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Molecular chaperone Tir
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9714
Polymers19,7311
Non-polymers2403
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Molecular chaperone Tir
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8112
Polymers19,7311
Non-polymers801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.931, 72.931, 217.541
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Molecular chaperone Tir


Mass: 19731.369 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: D3C88_25450 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A136TBS2
#2: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Br / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 51.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 30% PEG Smear Broad, 10% ethylene glycol, 0.1 M potassium sodium tartrate tetrahydrate, 0.1 M sodium cacodylate pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.98→46.6 Å / Num. obs: 41733 / % possible obs: 99.7 % / Redundancy: 52.5 % / Biso Wilson estimate: 25.73 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.018 / Rrim(I) all: 0.133 / Net I/σ(I): 35.5
Reflection shellResolution: 1.98→2.03 Å / Rmerge(I) obs: 1.271 / Num. unique obs: 2767 / CC1/2: 0.912 / Rpim(I) all: 0.173 / Rrim(I) all: 1.283

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.98→46.6 Å / SU ML: 0.1576 / Cross valid method: FREE R-VALUE / σ(F): 0.12 / Phase error: 20.6167
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2262 1951 4.84 %
Rwork0.1814 38328 -
obs0.1836 40279 96.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.41 Å2
Refinement stepCycle: LAST / Resolution: 1.98→46.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3992 0 7 246 4245
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01064080
X-RAY DIFFRACTIONf_angle_d0.98745513
X-RAY DIFFRACTIONf_chiral_restr0.056607
X-RAY DIFFRACTIONf_plane_restr0.0089703
X-RAY DIFFRACTIONf_dihedral_angle_d13.8241514
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.030.26411130.1912406X-RAY DIFFRACTION86.18
2.03-2.090.22871380.17182550X-RAY DIFFRACTION92.28
2.09-2.150.21851300.16522634X-RAY DIFFRACTION93.89
2.15-2.220.22561260.16472629X-RAY DIFFRACTION95.07
2.22-2.30.23741300.16962705X-RAY DIFFRACTION96
2.3-2.390.24531410.16852674X-RAY DIFFRACTION96.31
2.39-2.50.24291340.17342746X-RAY DIFFRACTION97.36
2.5-2.630.21571400.19142726X-RAY DIFFRACTION97.12
2.63-2.790.23291540.18922756X-RAY DIFFRACTION97.98
2.79-3.010.23751500.18812795X-RAY DIFFRACTION99.06
3.01-3.310.21951480.19152849X-RAY DIFFRACTION99.37
3.31-3.790.23191490.18252847X-RAY DIFFRACTION99.53
3.79-4.780.19311380.15682922X-RAY DIFFRACTION99.61
4.78-46.60.23651600.20863089X-RAY DIFFRACTION99.6

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